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- PDB-5d21: Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseu... -

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Basic information

Entry
Database: PDB / ID: 5d21
TitleMultivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas aeruginosa Biofilms Targeting Lectin LecA
ComponentsLecA
KeywordsSUGAR BINDING PROTEIN / Lectin / Pseudomonas / Multivalency / Antimicrobial / Biofilm
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding lectin / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
phenyl beta-D-galactopyranoside / PA-I galactophilic lectin / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBergmann, M. / Michaud, G. / Visini, R. / Jin, X. / Stocker, A. / Darbre, T. / Reymond, J.-L.
CitationJournal: Org.Biomol.Chem. / Year: 2016
Title: Multivalency effects on Pseudomonas aeruginosa biofilm inhibition and dispersal by glycopeptide dendrimers targeting lectin LecA.
Authors: Bergmann, M. / Michaud, G. / Visini, R. / Jin, X. / Gillon, E. / Stocker, A. / Imberty, A. / Darbre, T. / Reymond, J.L.
History
DepositionAug 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LecA
B: LecA
C: LecA
D: LecA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,26612
Polymers51,0814
Non-polymers1,1858
Water13,511750
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-4 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.539, 72.940, 79.008
Angle α, β, γ (deg.)117.510, 104.900, 89.910
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
LecA / Lectin / PA-I galactophilic lectin / Pseudomonas aeruginosa genome assembly PAE221


Mass: 12770.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecA, pa1L, ERS445055_02484, PA257_2995, PA8380_27900, PAE221_02397, PAMH19_6043, YQ19_15530
Production host: Escherichia coli (E. coli) / References: UniProt: A0A073A1F3, UniProt: Q05097*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-56N / phenyl beta-D-galactopyranoside / phenyl beta-D-galactoside / phenyl D-galactoside / phenyl galactoside


Type: D-saccharide / Mass: 256.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H16O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 750 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 1.5M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.9→67.083 Å / Num. all: 57986 / Num. obs: 57986 / % possible obs: 95.6 % / Redundancy: 3 % / Biso Wilson estimate: 9.25 Å2 / Rpim(I) all: 0.043 / Rrim(I) all: 0.079 / Rsym value: 0.066 / Net I/av σ(I): 7.729 / Net I/σ(I): 9 / Num. measured all: 176263
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-23.10.1653.32584683960.1040.1655.994.6
2-2.122.70.0954.32144780880.070.0956.395.5
2.12-2.272.90.1463.52130973410.0930.1467.493.6
2.27-2.4530.0866.72082768600.0560.0867.293.9
2.45-2.692.80.0747.41823764610.0520.0748.796.5
2.69-33.40.0718.61991958960.0440.07110.997.1
3-3.473.40.069.61815352840.0370.061397.5
3.47-4.253.30.04513.11456343900.0280.04513.897.4
4.25-6.0130.025231032934650.0180.02512.998.2
6.01-17.9023.10.02718.1563318050.0180.02712.994.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLM3.3.21data reduction
SCALA3.3.21data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OKO

1oko


Resolution: 1.9→17.902 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 2946 5.18 %
Rwork0.2097 53935 -
obs0.2105 56881 93.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.53 Å2 / Biso mean: 16.6386 Å2 / Biso min: 1.64 Å2
Refinement stepCycle: final / Resolution: 1.9→17.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 76 750 4430
Biso mean--21.15 26.75 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033779
X-RAY DIFFRACTIONf_angle_d0.7185171
X-RAY DIFFRACTIONf_chiral_restr0.027565
X-RAY DIFFRACTIONf_plane_restr0.004682
X-RAY DIFFRACTIONf_dihedral_angle_d12.3461275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93110.50511520.44562628278095
1.9311-1.96430.45011270.36952194232182
1.9643-20.2213890.25572574266392
2-2.03840.22511530.18692648280195
2.0384-2.080.25841310.18892587271895
2.08-2.12510.20091290.18412646277595
2.1251-2.17450.2021490.19622498264795
2.1745-2.22880.27261070.27712182228979
2.2288-2.28890.3151180.34862477259591
2.2889-2.35610.26111490.25692374252386
2.3561-2.4320.19071160.20562648276496
2.432-2.51870.24671240.18662646277096
2.5187-2.61920.21751610.17632631279297
2.6192-2.7380.16891890.18792611280097
2.738-2.88180.21091650.19332637280297
2.8818-3.06160.28061200.18862655277597
3.0616-3.29660.2061510.17722671282297
3.2966-3.62590.17721520.16692669282197
3.6259-4.14480.20941340.15532636277097
4.1448-5.20070.14871650.14682672283798
5.2007-17.90310.15571650.19152651281698

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